The computer-generated designs are bigger than the player-generated for reasons I do not quite know/remember. Likely there just needs to be a reason for the computer-ships to not be perfectly obsolete compared to what a the player can do.

It all adds up though, as the player can thus stick to creating the special ships. And the fact that you can swindle the AI. Build a ship with a Colony module on it, or Trade or Construction (I do not recall the best one), make sure there's one single weapon equipped and then fire up it's defenses so far as you can, preferably three different editions of this particular ship for different weapon types. When you fight, the AI will go for that ship and that ship alone, meaning that as long as the defenses hold, all your other ships are free to pound away on the enemy.

That being said though, having automatically superior designs avaible kind of takes the fun out of making ships.

If I recall correctly, the reason I heard was the AI ship designer doesn't resize parts before fitting them onto the hull. Parts are normally resized before being fited onto a ship, which causes them to become larger. In many cases, the increase might be as large as 3 or 4 points, though some ship modules can be much, much more. Because the AI ship designer isn't resizing ship parts when they place them, you are getting ships fitted with more equipment than it should be fited with.

By the way, didn't they fix this bug? What version of the game are you using?